diff --git a/docs/source/index.rst b/docs/source/index.rst
index 22f2824a28464a6682accc09937e9b54b1d15534..62dfb486b3f34d5a187cbaaba46a51c3d1642ca0 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -35,7 +35,6 @@ MOOSE is a simulation environment, not just a numerical engine: It provides data
.. toctree::
:maxdepth: 1
-
:titlesonly:
.. toctree::
diff --git a/docs/source/install/install.rst b/docs/source/install/install.rst
index d298bdec3720ea8344e886ec9459413f519746ed..6d83001c30d57a9cbe04f831d40f49bdcae2e714 100644
--- a/docs/source/install/install.rst
+++ b/docs/source/install/install.rst
@@ -45,7 +45,8 @@ In case your distribution is not listed on `our repository page
First, you need to get the source code. You can use ``git`` (clone the
repository) or download snapshot of github repo by clicking on `this link
-<https://github.com/BhallaLab/moose/archive/master.zip>`_.::
+<https://github.com/BhallaLab/moose/archive/master.zip>`__.
+::
$ git clone https://github.com/BhallaLab/moose
@@ -57,7 +58,7 @@ Or,
$ unzip master.zip
If you don't want latest snapshot of ``MOOSE``, you can download other released
-versions from `here <`https://github.com/BhallaLab/moose/releases>`_.
+versions from `here <https://github.com/BhallaLab/moose/releases>`__.
Install dependencies
^^^^^^^^^^^^^^^^^^^^
@@ -157,8 +158,8 @@ If you have installed the pre-built package, then you already have the GUI.
You can launch it by runnung `moosegui` command in terminal.
You can get the source of ``moose-gui`` from `here
-<https://github.com/BhallaLab/moose-gui>`_. You can download it either by
-clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`_
+<https://github.com/BhallaLab/moose-gui>`__. You can download it either by
+clicking on `this link <https://github.com/BhallaLab/moose-gui/archive/master.zip>`__
or by using ``git`` ::
$ git clone https://github.com/BhallaLab/moose-gui
@@ -203,7 +204,7 @@ Building moogli
---------------
``moogli`` is subproject of ``MOOSE`` for visualizing models. More details can
-be found `here <http://moose.ncbs.res.in/moogli>`_.
+be found `here <http://moose.ncbs.res.in/moogli>`__.
`Moogli` is part of `moose` package. Building moogli can be tricky because of
multiple depednecies it has.
@@ -212,7 +213,7 @@ multiple depednecies it has.
- OSG (3.2.x) For 3D rendering and simulation of neuronal models
- Qt4 (4.8.x) For C++ GUI of Moogli
-To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`_.
+To get the latest source code of ``moogli``, click on `this link <https://github.com/BhallaLab/moogli/archive/master.zip>`__.
Moogli depends on ``OpenSceneGraph`` (version 3.2.0 or higher) which may not
be easily available for your operating system.
diff --git a/docs/source/user/py/cookbook/Rd.rst b/docs/source/user/py/cookbook/Rd.rst
index 04836369a2dc26c4b535b9bf3a3324d14106e9af..625b8bc819cf5b695210c854050e7630d60c6ff0 100644
--- a/docs/source/user/py/cookbook/Rd.rst
+++ b/docs/source/user/py/cookbook/Rd.rst
@@ -1104,11 +1104,9 @@ the location of the spine. There are three pulses of calcium, the first
being quite weak.
.. figure:: ../../../../images/rdes10_CaSpread.png
- :alt: Calcium influx from spine in middle of cylindrical compartment,
- spreading into the dendrite and then axially in both directions.
+ :alt: Calcium influx from spine in middle of cylindrical compartment, spreading into the dendrite and then axially in both directions.
- Calcium influx from spine in middle of cylindrical compartment,
- spreading into the dendrite and then axially in both directions.
+ Calcium influx from spine in middle of cylindrical compartment, spreading into the dendrite and then axially in both directions.
Once the simulation completes you'll also see a number of plots, so that
you can figure out what the calcium influx was doing. Here, we have a
diff --git a/docs/source/user/py/cookbook/chem_GUI.rst b/docs/source/user/py/cookbook/chem_GUI.rst
index 390b56ee104ab200ada187c945987ffc3959d8a5..543f48c6b34abb7ecc4da7d71d4f7f822221f06b 100644
--- a/docs/source/user/py/cookbook/chem_GUI.rst
+++ b/docs/source/user/py/cookbook/chem_GUI.rst
@@ -355,6 +355,7 @@ variables can be input from pool object.
- **New**: **File -> New -> Model name**. This opens a empty widget for model building
- **Saving models**: **File -> Save Model -> select from dialog**.
- **Changing numerical methods**: **Preference->Chemical tab** item from Simulation Control. Currently supports:
+
1. Runge Kutta: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
2. Gillespie: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
3. Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
diff --git a/docs/source/user/py/cookbook/elec_sim_eg.rst b/docs/source/user/py/cookbook/elec_sim_eg.rst
index 0506b94c093caaf775b3a3fc0e0399c931718772..224cf913e7c5429701ef78692b5a0fd31ab08862 100644
--- a/docs/source/user/py/cookbook/elec_sim_eg.rst
+++ b/docs/source/user/py/cookbook/elec_sim_eg.rst
@@ -53,8 +53,9 @@ Insert Spine heads
.. automodule:: insertSpinesWithoutRdesigneur
:members:
-Multi compartmental Neuron model
---------------------------------
+.. Multi compartmental Neuron model
+.. --------------------------------
-.. automodule:: testHsolve
+.. automodule: testHsolve
:members:
+ (testHsolve no longer exists in any of the appended paths)
diff --git a/docs/source/user/py/cookbook/multi_sim_eg.rst b/docs/source/user/py/cookbook/multi_sim_eg.rst
index 564bdb7fab6c5ae715e87a6e84405dc0fc36ca57..529ee4c3911a9729ba3db76dfe404330b6823cec 100644
--- a/docs/source/user/py/cookbook/multi_sim_eg.rst
+++ b/docs/source/user/py/cookbook/multi_sim_eg.rst
@@ -20,5 +20,6 @@ Modeling chemical reactions in neurons
.. automodule:: gssaRDspiny
:members:
-.. automodule:: rxdSpineSize
+.. automodule: rxdSpineSize
:members:
+ (rxdSpineSize does not exist in any appended folders -> gives error while building html)
diff --git a/docs/source/user/py/quickstart/classes_demos.rst b/docs/source/user/py/quickstart/classes_demos.rst
index d8e3bb3493861f7edbb7991735d0158fe0e53503..290c2eb70994a5b2a4857ff00500dfad83782f19 100644
--- a/docs/source/user/py/quickstart/classes_demos.rst
+++ b/docs/source/user/py/quickstart/classes_demos.rst
@@ -70,6 +70,7 @@ Function
.. automodule:: func
:members:
+ :noindex:
SymCompartment
^^^^^^^^^^^^^^
diff --git a/docs/source/user/py/quickstart/moose_quickstart.rst b/docs/source/user/py/quickstart/moose_quickstart.rst
index 1df78de7d9c24c9e8d33eb18c43710b40b8d5a5d..55b30186fe2adcefe4cace233b7cc287a0cef017 100644
--- a/docs/source/user/py/quickstart/moose_quickstart.rst
+++ b/docs/source/user/py/quickstart/moose_quickstart.rst
@@ -2,10 +2,6 @@
Getting started with python scripting for MOOSE
***********************************************
-.. contents:
- :local:
- :depth: 1
-
.. figure:: ../../../images/Gallery_Moose_Multiscale.png
:alt: **multiple scales in moose**
:scale: 100%
@@ -30,11 +26,10 @@ MOOSE is a simulation environment, not just a numerical engine: It provides data
Contents:
-.. toctree::
- :maxdepth: 2
- :numbered:
+.. contents::
+ :local:
+ :depth: 1
- moose_quickstart
Coding basics and how to use this document
==========================================
@@ -114,6 +109,7 @@ Alternatively, if you want to see a full list of classes, functions and their fi
* :ref:`genindex`
* :ref:`modindex`
+
..
:ref:`search`
diff --git a/moose-examples/snippets/crossComptNeuroMesh.py b/moose-examples/snippets/crossComptNeuroMesh.py
index a96081392c3f4127b807f7dbe70b6a15aedc1155..a0b7958b5ca997cde7989194f228c84f87facb9b 100644
--- a/moose-examples/snippets/crossComptNeuroMesh.py
+++ b/moose-examples/snippets/crossComptNeuroMesh.py
@@ -204,7 +204,7 @@ def main():
files. Normally one uses standard model formats like
SBML or kkit to concisely define kinetic and neuronal models.
This example creates a simple reaction::
- a <==> b <==> c
+ a <==> b <==> c
in which **a, b**, and **c** are in the dendrite, spine head, and PSD
respectively.
The model is set up to run using the Ksolve for integration. Although
diff --git a/moose-examples/snippets/loadSbmlmodel.py b/moose-examples/snippets/loadSbmlmodel.py
index 3237cfedacbe68cef50f32640b9485081a5b012b..f32e6c0ebd385064c0f26095b27ab482aebf66d5 100644
--- a/moose-examples/snippets/loadSbmlmodel.py
+++ b/moose-examples/snippets/loadSbmlmodel.py
@@ -46,12 +46,12 @@ from moose.chemUtil.add_Delete_ChemicalSolver import *
def main():
"""
-This example illustrates loading, running of an SBML model defined in XML format.
-Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
-Plots are setup.
-Model is run for 20sec.
-As a general rule we created model under '/path/model' and plots under '/path/graphs'.
-If someone wants to load anyother file then
+ This example illustrates loading, running of an SBML model defined in XML format.
+ Default this file load's 00001-sbml-l3v1.xml which is taken from l3v1 SBML testcase.
+ Plots are setup.
+ Model is run for 20sec.
+ As a general rule we created model under '/path/model' and plots under '/path/graphs'.
+ If someone wants to load anyother file then
`python loadSbmlmodel filepath runtime`
"""